3-183829177-C-T

Position:

• chr3-183829177-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_005247582.6(PARL):​c.1029-2445G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 240,300 control chromosomes in the GnomAD database, including 61,412 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.70 (37448 hom., cov: 31)
  • Exomes 𝑓: 0.73 (23964 hom.)
• Consequence: PARL XM_005247582.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521

Genes affected

PARL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARL	XM_005247582.6	c.1029-2445G>A		intron_variant
PARL	XM_017006800.3	c.927-2445G>A		intron_variant
PARL	XM_017006801.2	c.879-2445G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105856 AN: 151870 Hom.: 37416 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.726

GnomAD4 exome AF: 0.729 AC: 64357 AN: 88312 Hom.: 23964 AF XY: 0.729 AC XY: 33553 AN XY: 46014

Gnomad4 AFR exome AF: 0.617

Gnomad4 AMR exome AF: 0.807

Gnomad4 ASJ exome AF: 0.814

Gnomad4 EAS exome AF: 0.962

Gnomad4 SAS exome AF: 0.702

Gnomad4 FIN exome AF: 0.633

Gnomad4 NFE exome AF: 0.712

Gnomad4 OTH exome AF: 0.730

GnomAD4 genome AF: 0.697 AC: 105934 AN: 151988 Hom.: 37448 Cov.: 31 AF XY: 0.691 AC XY: 51369 AN XY: 74292

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.731

Alfa AF: 0.727 Hom.: 38984

Bravo AF: 0.710

Asia WGS AF: 0.839 AC: 2920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.77
DANN	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs263003; hg19: chr3-183546965;